title: Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
abstract: Epidemiology and candidate gene studies indicate a shared genetic basis for celiac disease (CD) and rheumatoid arthritis (RA), but the extent of this sharing has not been systematically explored. Previous studies demonstrate that 6 of the established non-HLA CD and RA risk loci (out of 26 loci for each disease) are shared between both diseases. We hypothesized that there are additional shared risk alleles and that combining genome-wide association study (GWAS) data from each disease would increase power to identify these shared risk alleles. We performed a meta-analysis of two published GWAS on CD (4,533 cases and 10,750 controls) and RA (5,539 cases and 17,231 controls). After genotyping the top associated SNPs in 2,169 CD cases and 2,255 controls, and 2,845 RA cases and 4,944 controls, 8 additional SNPs demonstrated P<5 × 10(-8) in a combined analysis of all 50,266 samples, including four SNPs that have not been previously confirmed in either disease: rs10892279 near the DDX6 gene (P(combined) =  1.2 × 10(-12)), rs864537 near CD247 (P(combined) =  2.2 × 10(-11)), rs2298428 near UBE2L3 (P(combined) =  2.5 × 10(-10)), and rs11203203 near UBASH3A (P(combined) =  1.1 × 10(-8)). We also confirmed that 4 gene loci previously established in either CD or RA are associated with the other autoimmune disease at combined P<5 × 10(-8) (SH2B3, 8q24, STAT4, and TRAF1-C5). From the 14 shared gene loci, 7 SNPs showed a genome-wide significant effect on expression of one or more transcripts in the linkage disequilibrium (LD) block around the SNP. These associations implicate antigen presentation and T-cell activation as a shared mechanism of disease pathogenesis and underscore the utility of cross-disease meta-analysis for identification of genetic risk factors with pleiotropic effects between two clinically distinct diseases.
authors.affiliation: Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Zhernakova
authors.forename: Eli A
authors.initials: EA
authors.lastname: Stahl
authors.forename: Gosia
authors.initials: G
authors.lastname: Trynka
authors.forename: Soumya
authors.initials: S
authors.lastname: Raychaudhuri
authors.forename: Eleanora A
authors.initials: EA
authors.lastname: Festen
authors.forename: Lude
authors.initials: L
authors.lastname: Franke
authors.forename: Harm-Jan
authors.initials: HJ
authors.lastname: Westra
authors.forename: Rudolf S N
authors.initials: RS
authors.lastname: Fehrmann
authors.forename: Fina A S
authors.initials: FA
authors.lastname: Kurreeman
authors.forename: Brian
authors.initials: B
authors.lastname: Thomson
authors.forename: Namrata
authors.initials: N
authors.lastname: Gupta
authors.forename: Jihane
authors.initials: J
authors.lastname: Romanos
authors.forename: Ross
authors.initials: R
authors.lastname: McManus
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Ryan
authors.forename: Graham
authors.initials: G
authors.lastname: Turner
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Brouwer
authors.forename: Marcel D
authors.initials: MD
authors.lastname: Posthumus
authors.forename: Elaine F
authors.initials: EF
authors.lastname: Remmers
authors.forename: Francesca
authors.initials: F
authors.lastname: Tucci
authors.forename: Rene
authors.initials: R
authors.lastname: Toes
authors.forename: Elvira
authors.initials: E
authors.lastname: Grandone
authors.forename: Maria Cristina
authors.initials: MC
authors.lastname: Mazzilli
authors.forename: Anna
authors.initials: A
authors.lastname: Rybak
authors.forename: Bozena
authors.initials: B
authors.lastname: Cukrowska
authors.forename: Marieke J H
authors.initials: MJ
authors.lastname: Coenen
authors.forename: Timothy R D J
authors.initials: TR
authors.lastname: Radstake
authors.forename: Piet L C M
authors.initials: PL
authors.lastname: van Riel
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Li
authors.forename: Paul I W
authors.initials: PI
authors.lastname: de Bakker
authors.forename: Peter K
authors.initials: PK
authors.lastname: Gregersen
authors.forename: Jane
authors.initials: J
authors.lastname: Worthington
authors.forename: Katherine A
authors.initials: KA
authors.lastname: Siminovitch
authors.forename: Lars
authors.initials: L
authors.lastname: Klareskog
authors.forename: Tom W J
authors.initials: TW
authors.lastname: Huizinga
authors.forename: Cisca
authors.initials: C
authors.lastname: Wijmenga
authors.forename: Robert M
authors.initials: RM
authors.lastname: Plenge
mesh_terms: D000483:Alleles; D001172:Arthritis, Rheumatoid / Q000235:genetics* / Q000276:immunology; D002446:Celiac Disease / Q000235:genetics* / Q000276:immunology; D056426:Genetic Loci; D055106:Genome-Wide Association Study; D006649:Histocompatibility Antigens / Q000235:genetics; D008213:Lymphocyte Activation; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D013601:T-Lymphocytes / Q000276:immunology / Q000378:metabolism
chemical_list: D006649:Histocompatibility Antigens